814 research outputs found
Deformations of highly symmetric Calabi-Yau Grassmannian hypersurfaces (computational tools)
No full text<p>This file provides SageMath worksheets and records of Magma sessions associated with the paper "Deformations of highly symmetric Calabi-Yau Grassmannian hypersurfaces" by Adriana Salerno, Ursula Whitcher, and Chenglong Yu.</p>
Questionnaire Interview to Dr. Chenglong Yu_Regeneration of Liangzhu Culture
No full textThis questionnaire interview was conducted for the article "Regeneration of Liangzhu Culture through Innovative Exhibition Methods and Technologies and Integrations with Cultural and Economic Developments". It was finished by Dr. Chenglong Yu in Nanjing Museum, in June 2020. The questions include topics like cultural innovative products, simulative restoration and interactive activities
Global comparison of multiple-segmented viruses in 12-dimensional genome space
No full textAbstract not availableHsin-Hsiung Huang, Chenglong Yu, Hui Zheng, Troy Hernandez, Shek-Chung Yau, Rong Lucy He, Jie Yang, Stephen S.-T. Ya
A new method to cluster DNA sequences using Fourier power spectrum
No full textData source: Supplementary material, https://doi.org/10.1016/j.jtbi.2015.02.026
Link to a related website: http://europepmc.org/articles/pmc7094126?pdf=render, Open Access via UnpaywallAbstract not availableTung Hoang, Changchuan Yin, Hui Zheng, Chenglong Yu, Rong Lucy He,
Stephen S.-T.Ya
Quantifying grain size distribution of pedogenic magnetic particles in Chinese loess and its significance for pedogenesis
No full textQuaternary glacial/interglacial cycles have been imprinted on the Chinese loess/paleosol sequences through pedogenesis. In order to accurately decode the paleoclimatic signals carried by these pedogenic particles it is essential to quantify the pedogenically produced magnetic particles in terms of mineralogy as well as grain size distribution (GSD). To date, the GSD has not been accurately determined because of the dearth of available means for analyzing extremely fine grained (nanometer-scale) pedogenic magnetic particles. Using low-temperature techniques, we systematically investigated the temperature dependency of χfd (defined as χ1Hz − χ10Hz, where χ1Hz and χ10Hz are AC magnetic susceptibility measured at 1 and 10 Hz, respectively) from two characteristic loess profiles, one located at the western Chinese Loess Plateau and the other in the central plateau. On the basis of Néel theory for a shape anisotropy dominant grain and experimental analysis at low temperatures, a quantitative GSD for pedogenic particles in Chinese loess/paleosols was constructed. We found that the dominant magnetic grain size lies just above the superparamagnetic/single-domain threshold (~20–25 nm) and that the GSD is almost independent of the degree of pedogenesis. This observation agrees well with other constraints from previous studies. This new GSD model improves our understanding of the pedogenic processes in Chinese loess, enabling further explicit linkage of environmental magnetism to paleoclimate changes
Clustering DNA sequences using the out-of-place measure with reduced n-grams
No full textData source: supplementary material, https://doi.org/10.1016/j.jtbi.2016.06.029The alignment-free n-gram based method with the out-of-place measures as the distance has been successfully applied to automatic text or natural languages categorization in real time. However, it is not clear about its performance and the selection of n for comparing genome sequences. Here we propose a symmetric version of the out-of-place measure and a new approach for finding the optimal range of n to construct a phylogenetic tree with the symmetric out-of-place measures. Our method is then applied to real genome sequence datasets. The resulting phylogenetic trees are matching with the standard biological classification. It shows that our proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.Hsin-Hsiung Huang, Chenglong Y
Virus database and online inquiry system based on natural vectors
No full textWe construct a virus database called VirusDB (http://yaulab.math.tsinghua.edu.cn/VirusDB/) and an online inquiry system to serve people who are interested in viral classification and prediction. The database stores all viral genomes, their corresponding natural vectors, and the classification information of the single/multiple-segmented viral reference sequences downloaded from National Center for Biotechnology Information. The online inquiry system serves the purpose of computing natural vectors and their distances based on submitted genomes, providing an online interface for accessing and using the database for viral classification and prediction, and back-end processes for automatic and manual updating of database content to synchronize with GenBank. Submitted genomes data in FASTA format will be carried out and the prediction results with 5 closest neighbors and their classifications will be returned by email. Considering the one-to-one correspondence between sequence and natural vector, time efficiency, and high accuracy, natural vector is a significant advance compared with alignment methods, which makes VirusDB a useful database in further research.Rui Dong, Hui Zheng, Kun Tian, Shek-Chung Yau, Weiguang Mao, Wenping Yu, Changchuan Yin, Chenglong Yu, Rong Lucy He, Jie Yang, Stephen ST Ya
Synthesis and Electroluminescence of Thieno-[3,4-b]pyrazine-cored Molecule with Fluorinated Shell.pdf
No full textPolybrominated diphenyl ethers (PBDEs) are a class of brominated flame-retardants (BFRs) that are widely used in industrial products and have posed potential risk on the coastal environment of the Laizhou Bay in China. They are of great concern due to their toxicities, such as hepatotoxicity, carcinogenecity, neurotoxicity, immunotoxicity and endocrine disrupting effects in animals. In this work, we focused on the gender-specific responses of BDE 47 in mussel Mytilus galloprovincialis using a combined proteomic and metabolomic approach. Metabolic responses indicated that BDE 47 mainly caused disturbance in energy metabolism in male mussel gills. For female mussel samples, disruption in both osmotic regulation and energy metabolism was found in terms of differential metabolic profiles. Proteomic responses revealed that BDE 47 induced cell apoptosis and reduced reactive oxygen species (ROS) production in both male and female mussels, disturbance in protein homeostasis in male mussels as well as disturbance in female mussel proteolysis based on the differential proteomic biomarkers. Overall, these results confirmed the gender-specific responses in mussels to ODE 47 exposures. This work demonstrated that an integrated metabolomic and proteomic approach could provide an important insight into the toxicological effects of environmental pollutant to organisms. (C) 2013 Elsevier B.V. All rights reserved.Polybrominated diphenyl ethers (PBDEs) are a class of brominated flame-retardants (BFRs) that are widely used in industrial products and have posed potential risk on the coastal environment of the Laizhou Bay in China. They are of great concern due to their toxicities, such as hepatotoxicity, carcinogenecity, neurotoxicity, immunotoxicity and endocrine disrupting effects in animals. In this work, we focused on the gender-specific responses of BDE 47 in mussel Mytilus galloprovincialis using a combined proteomic and metabolomic approach. Metabolic responses indicated that BDE 47 mainly caused disturbance in energy metabolism in male mussel gills. For female mussel samples, disruption in both osmotic regulation and energy metabolism was found in terms of differential metabolic profiles. Proteomic responses revealed that BDE 47 induced cell apoptosis and reduced reactive oxygen species (ROS) production in both male and female mussels, disturbance in protein homeostasis in male mussels as well as disturbance in female mussel proteolysis based on the differential proteomic biomarkers. Overall, these results confirmed the gender-specific responses in mussels to ODE 47 exposures. This work demonstrated that an integrated metabolomic and proteomic approach could provide an important insight into the toxicological effects of environmental pollutant to organisms. (C) 2013 Elsevier B.V. All rights reserved
Control of finite-time anti-synchronization for variable-order fractional chaotic systems with unknown parameters
No full textFractional-order chaotic system with variable-order and unknown parameters, as an excellent tool to describe the memory and hereditary characteristics of the complex phenomena in reality, remains important, but nowadays there exist few results about this system. This paper presents a finite-time anti-synchronization of two these systems based on the Mittag-Leffler stable theory and norm theory, in which the order varies with time and the unknown parameters of the systems are estimated. Moreover, a corollary about the monotone effect of variable order on the norm of the error system is deduced. We take different nonlinear variable orders for two identical Lü fractional chaotic systems and for two different Lü and Chen-Lee fractional chaotic systems as examples. The simulations illustrate the effectiveness and feasibility of the proposed control scheme.Li Zhang, Chenglong Yu, Tao Li
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